Dear friends , Hi ( I'm not native in English so, be ready for some possible language flaws)
I have 3 healthy and 3 un-healthy fish transcriptome sequences (illumina paired-end) and I have used Trinity software to de novo assemble them.
Now I want to collect those genes that are totally present in one condition (e.g healthy) and totally absent in the second condition (I have used DESeq2 for DEG analysis). but the problem is this that usually there is several isoforms for each transcripts in Trinity result and even when one isoform of one gene has absnt/present manner, the other isoforms may have the same expression.
My finall goal is to find transcripts or genes that I can use them as marker for health/illness determination using normal PCR (not qPCR).
Thank you in advance